src/gromacs/essentialdynamics/edsam.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 /*! \libinternal \file
  39  *
  40  * \brief
  41  * Declares functions to calculate both essential dynamics constraints
  42  * as well as flooding potentials and forces.
  43  *
  44  * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
  45  * Carsten Kutzner <ckutzne@gwdg.de>
  46  *
  47  * \inlibraryapi
  48  */
  49 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
  50 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
  51
  52 #include <memory>
  53
  54 #include "gromacs/math/vectypes.h"
  55 #include "gromacs/utility/basedefinitions.h"
  56 #include "gromacs/utility/classhelpers.h"
  57
  58 /*! \brief Abstract type for essential dynamics
  59  *
  60  * The main type is defined only in edsam.cpp
  61  */
  62 struct gmx_edsam;
  63 struct gmx_domdec_t;
  64 struct gmx_mtop_t;
  65 struct gmx_output_env_t;
  66 struct ObservablesHistory;
  67 struct t_commrec;
  68 struct t_filenm;
  69 struct t_inputrec;
  70 class t_state;
  71
  72 namespace gmx
  73 {
  74 enum class StartingBehavior;
  75 class Constraints;
  76 class EssentialDynamics
  77 {
  78 public:
  79     EssentialDynamics();
  80     ~EssentialDynamics();
  81
  82     /*! \brief Getter for working data
  83      *
  84      * This is needed while the module is still under
  85      * construction. */
  86     gmx_edsam* getLegacyED();
  87
  88 private:
  89     class Impl;
  90
  91     PrivateImplPointer<Impl> impl_;
  92 };
  93 class MDLogger;
  94 } // namespace gmx
  95
  96 /*! \brief Applies essential dynamics constrains as defined in the .edi input file.
  97  *
  98  * \param ir                MD input parameter record.
  99  * \param step              Number of the time step.
 100  * \param cr                Data needed for MPI communication.
 101  * \param xs                The local positions on this processor.
 102  * \param v                 The local velocities.
 103  * \param box               The simulation box.
 104  * \param ed                The essential dynamics data.
 105  */
 106 void do_edsam(const t_inputrec* ir,
 107               int64_t           step,
 108               const t_commrec*  cr,
 109               rvec              xs[],
 110               rvec              v[],
 111               const matrix      box,
 112               gmx_edsam*        ed);
 113
 114
 115 /*! \brief Initializes the essential dynamics and flooding module.
 116  *
 117  * \param mdlog             Logger.
 118  * \param ediFileName       Essential dynamics input file.
 119  * \param edoFileName       Output file for essential dynamics data.
 120  * \param mtop              Molecular topology.
 121  * \param ir                MD input parameter record.
 122  * \param cr                Data needed for MPI communication.
 123  * \param constr            Data structure keeping the constraint information.
 124  * \param globalState       The global state, only used on the master rank.
 125  * \param oh                The observables history container.
 126  * \param oenv              The output environment information.
 127  * \param startingBehavior  Describes whether this is a restart appending to output files
 128  *
 129  * \returns                 A pointer to the ED data structure.
 130  */
 131 std::unique_ptr<gmx::EssentialDynamics> init_edsam(const gmx::MDLogger&    mdlog,
 132                                                    const char*             ediFileName,
 133                                                    const char*             edoFileName,
 134                                                    const gmx_mtop_t*       mtop,
 135                                                    const t_inputrec*       ir,
 136                                                    const t_commrec*        cr,
 137                                                    gmx::Constraints*       constr,
 138                                                    const t_state*          globalState,
 139                                                    ObservablesHistory*     oh,
 140                                                    const gmx_output_env_t* oenv,
 141                                                    gmx::StartingBehavior   startingBehavior);
 142
 143 /*! \brief Make a selection of the home atoms for the ED groups.
 144  *
 145  * Should be called at every domain decomposition.
 146  *
 147  * \param dd                Domain decomposition data.
 148  * \param ed                Essential dynamics and flooding data.
 149  */
 150 void dd_make_local_ed_indices(gmx_domdec_t* dd, gmx_edsam* ed);
 151
 152
 153 /*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
 154  *
 155  * \param cr                Data needed for MPI communication.
 156  * \param ir                MD input parameter record.
 157  * \param x                 Positions on the local processor.
 158  * \param force             Forcefield forces to which the flooding forces are added.
 159  * \param ed                The essential dynamics data.
 160  * \param box               The simulation box.
 161  * \param step              Number of the time step.
 162  * \param bNS               Are we in a neighbor searching step?
 163  */
 164 void do_flood(const t_commrec*  cr,
 165               const t_inputrec* ir,
 166               const rvec        x[],
 167               rvec              force[],
 168               gmx_edsam*        ed,
 169               const matrix      box,
 170               int64_t           step,
 171               gmx_bool          bNS);
 172
 173 #endif